Re: Calculating displacement in a system with periodic boundary

From: Eric H. Lee (
Date: Mon May 11 2009 - 23:49:25 CDT

You can choose not to wrap the system coordinates during the
simulation, but keeping the periodic boundary conditions in place.
The options in the namd script are "wrapall" and "wrapwater" I believe.

You might also try unwrapping your existing trajectory using PBCtools:


On May 11, 2009, at 11:26 PM, Fred (Rui FENG) wrote:

> Hi All,
> I have a question that can be simplified like this:
> Suppose there's a cube with lots of particles/atoms. The boundary is
> periodic and only Lennard Jones force field is in the system. All
> atoms are moving with random velocities. The velocity of the center
> of mass could not be zero. I have a common DCD file with coordinates
> of all atoms. My question is: how to get the displacement of all
> atoms?
> I cannot just simply subtract the coordinate of one atom from the
> coordinate of the same atom in the previous frame. Supposing the
> cube has 200 edge length and the center is (0,0,0). If a atom at the
> position (99, 0, 0) moves to the position (-99, 0, 0), the
> displacement could be either 2 or -198 because of the periodic
> boundary. The absolute coordinate could be (102, 0, 0), but in the
> DCD file it's (-99, 0, 0). It makes the displacement calculation
> impossible.
> So I was wondering if there are any ways with which NAMD can output
> a "modified" DCD file with absolute coordinates. Thank you!
> Have a nice day!
> Fred

Eric H. Lee
Medical Scholars Program
Theoretical and Computational Biophysics Group, UIUC

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